Cycles alpha mask hole
There are a couple issues. My first question is why are you using two scenes? That will really complicate things. In this answer I have only addressed one as you can copy that information to the second one.

The first thing I noticed is you have your makes layers set, and although that could be handy in many instances, it really is not necessary in this case. Go ahead and disable all of them on all render layers:



Also you should try and change your compositor setup, all you need is something like this:



This setup gives me a nice result, and the issues you mentioned appear to have been fixed.